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DSM giving Negative values even with GCP's

Hello, I tried to process the 2700 Image dataset captured from phantom RTK. I exported the results and the DSM and DTM has negative values. Values ranges from -40 to +20M. We conducted the DGPS survey at the same site and the values ranges from +6 to +50M. So, I used those DGPS points as the GCP’s and reprocessed the dataset but the results are still looking same. Can anyone please help me solve this issue. Thank You.

Hi Vikil,
We might need a little more information to help solve this issue. However it sounds like it could be an issue with your vertical coordinate system. What geoid are your GCPs in and what is your output vertical coordinates in?